Segmentation Fault

[Komal Rathi]

I am getting a Segmentation Fault error when running STAR v2.4.0d:

# STAR genome generation:

STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /mnt/isilon/cbmi/variome/reference/star_hg38 --genomeFastaFiles /mnt/isilon/cbmi/variome/reference/hg38/hg38_no_alt.fa --sjdbGTFfile /mnt/isilon/cbmi/variome/reference/gencode/v23/gencode.v23.annotation.gtf --sjdbOverhang 99

# STAR command:

STAR --runThreadN 4 --genomeDir /mnt/isilon/cbmi/variome/reference/star_hg38 --readFilesIn CHP134_R1.fastq.gz CHP134_R2.fastq.gz --readFilesCommand zcat --outFileNamePrefix CHP134_ --sjdbGTFfile /mnt/isilon/cbmi/variome/reference/gencode/v23/gencode.v23.annotation.gtf --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --quantMode TranscriptomeSAM --outSAMattributes NH HI AS NM MD --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --limitBAMsortRAM 32874361894

# Standard output:

Sep 20 14:28:09 ..... Started STAR run

Sep 20 14:30:19 ..... Started mapping

Sep 20 15:12:56 ..... Started sorting BAM

Max memory needed for sorting = 32874361894

# Standard error:

tmp.sh: line 1: 25953 Segmentation fault      STAR --runThreadN 4 --genomeDir /mnt/isilon/cbmi/variome/reference/star_hg38 --readFilesIn CHP134_R1.fastq.gz CHP134_R2.fastq.gz --readFilesCommand zcat --outFileNamePrefix CHP134_ --sjdbGTFfile /mnt/isilon/cbmi/variome/reference/gencode/v23/gencode.v23.annotation.gtf --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --quantMode TranscriptomeSAM --outSAMattributes NH HI AS NM MD --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --limitBAMsortRAM 32874361894

I am supplying the memory thats required for sorting as well,  I don't know what's going wrong here.

I am using the command based on what these people used: https://github.com/BD2KGenomics/toil-scripts/tree/master/src/toil_scripts/rnaseq_cgl#star

Thanks,

Komal

[Komal Rathi]

Updating to STAR 2.5.2b solved the problem.